Table 1

Binning of probes into specific pathogen signature probe sets

Pathogen
 Family
 Genome size (nt)
 Total tiling probes
 Top 20% AES* (a)
 GC content filter (b)
 Human genome filter (c)
 No. of filtered probes left (d = a - (b + c))
 No. of predicted cross-hybridizing probes (HD ≤ 4 and MCM ≥ 18) (e)
 No. of probes in pathogen r-signature (d + e)
1
 LCMV
 Arenaviridae
 10,056
 1,283
 348
 2
 8
 338
 0
 338
2
 Hantaan
 Bunyaviridae
 6,533
 834
 156
 5
 5
 146
 6
 152
3
 Sin Nombre
 Bunyaviridae
 6,562
 837
 182
 1
 2
 179
 6
 185
4
 229E
 Coronaviridae
 27,317
 3,495
 494
 11
 11
 472
 0
 472
5
 OC43
 Coronaviridae
 30,738
 3,937
 634
 15
 22
 597
 3
 600
6
 SARS
 Coronaviridae
 29,711
 3,805
 575
 8
 2
 565
 1
 566
7
 Dengue serotype 1
 Flaviviridae
 10,717
 1,370
 230
 2
 8
 220
 8
 228
8
 Dengue serotype 2
 Flaviviridae
 10,722
 1,370
 241
 0
 9
 232
 11
 243
9
 Dengue serotype 3
 Flaviviridae
 10,707
 1,370
 230
 0
 4
 226
 13
 239
10
 Dengue serotype 4
 Flaviviridae
 10,649
 1,361
 229
 1
 7
 221
 3
 224
11
 Japanese encephalitis
 Flaviviridae
 10,976
 1,404
 310
 3
 2
 305
 12
 317
12
 West Nile
 Flaviviridae
 10,962
 1,401
 320
 2
 2
 316
 9
 325
13
 Yellow fever
 Flaviviridae
 10,862
 1,389
 255
 2
 3
 250
 2
 252
14
 Hepatitis B
 Hepadnaviridae
 3,215
 409
 147
 14
 0
 133
 0
 133
15
 Influenza A†
 Orthomyxoviridae
 12,561
 1,582
 510
 1
 15
 494
 0
 494
16
 Influenza B
 Orthomyxoviridae
 14,452
 1,822
 665
 5
 18
 642
 2
 644
17
 Human papillomavirus type 10
 Papillomaviridae
 7,919
 1,011
 287
 16
 9
 262
 0
 262
18
 hMPV
 Paramyxoviridae
 13,335
 1,705
 322
 44
 17
 261
 0
 261
19
 Newcastle disease
 Paramyxoviridae
 15,186
 1,943
 329
 0
 2
 327
 3
 330
20
 Nipah
 Paramyxoviridae
 18,246
 2,335
 389
 12
 5
 372
 0
 372
21
 Parainfluenza 1
 Paramyxoviridae
 15,600
 1,995
 330
 8
 13
 309
 2
 311
22
 Parainfluenza 2
 Paramyxoviridae
 15,646
 2,002
 333
 10
 2
 321
 0
 321
23
 Parainfluenza 3
 Paramyxoviridae
 15,462
 1,979
 409
 28
 23
 358
 3
 361
24
 RSV B
 Paramyxoviridae
 15,225
 1,948
 383
 28
 4
 351
 4
 355
25
 Echovirus 1
 Picornaviridae
 7,397
 945
 238
 1
 10
 227
 22
 249
26
 Enterovirus A
 Picornaviridae
 7,413
 946
 193
 3
 0
 190
 8
 198
27
 Enterovirus B
 Picornaviridae
 7,389
 944
 179
 0
 4
 175
 22
 197
28
 Enterovirus C
 Picornaviridae
 7,401
 945
 183
 0
 0
 183
 4
 187
29
 Enterovirus D
 Picornaviridae
 7,390
 944
 155
 0
 3
 152
 8
 160
30
 Foot and mouth disease
 Picornaviridae
 8,115
 1,036
 194
 14
 3
 177
 0
 177
31
 Hepatitis A
 Picornaviridae
 7,478
 955
 163
 1
 6
 156
 0
 156
32
 Rhinovirus A (type 89)
 Picornaviridae
 7,152
 913
 191
 6
 6
 179
 1
 180
33
 Rhinovirus B
 Picornaviridae
 7,212
 920
 197
 2
 2
 193
 0
 193
34
 HIV 1
 Retroviridae
 9,181
 1,174
 191
 4
 0
 187
 0
 187
35
 Rubella
 Togaviridae
 9,755
 1,246
 117
 65
 0
 52
 0
 52
Total

419,242
 53,555


9768
9921

*AES scores for all tiling probes were ranked together and only those probes in the top 20th percentile were retained. †Segment 7 of Influenza A was omitted during probe design.

Wong et al. Genome Biology 2007 8:R93   doi:10.1186/gb-2007-8-5-r93

Open Data